copy of element copies element id

CHANGELOG

@@ -19,6 +19,8 @@ minerva (16.0.0~beta.1) stable; urgency=medium
     from the database (#1508)
   * Bug fix: adding user with already existing login and changing his
     privileges occured with error (#1507)
+  * Bug fix: export model as model could cause an issue (#1500, #1502)
+  * Bug fix: problem with export as image with data overlays (#1503, #1498)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 9 Jun 2021 15:00:00 +0200
 

model/src/main/java/lcsb/mapviewer/model/map/species/Element.java

@@ -280,6 +280,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
    *          original object that will be used for creating copy
    */
   protected Element(Element original) {
+    this.id = original.id;
     this.nameHorizontalAlign = original.getNameHorizontalAlign();
     this.nameVerticalAlign = original.getNameVerticalAlign();
     this.nameX = original.getNameX();

model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java

@@ -87,9 +87,11 @@ public class ElementTest extends ModelTestFunctions {
   @Test
   public void testConstructor() {
     GenericProtein protein = new GenericProtein();
+    protein.setId(-17);
     protein.setSubmodel(new ElementSubmodelConnection());
     Element copy = new GenericProtein(protein);
     assertNotNull(copy);
+    assertEquals(protein.getId(), copy.getId());
   }
 
   @Test

rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java

@@ -16,7 +16,8 @@ import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.commands.*;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.converter.*;
+import lcsb.mapviewer.converter.Converter;
+import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
 import lcsb.mapviewer.converter.graphics.DrawingException;
 import lcsb.mapviewer.converter.graphics.ImageGenerators;
@@ -59,8 +60,9 @@ public class ModelRestImpl extends BaseRestImpl {
   private Logger logger = LogManager.getLogger();
 
   @Autowired
-  public ModelRestImpl(IProjectBackgroundService projectBackgroundService) {
+  public ModelRestImpl(IProjectBackgroundService projectBackgroundService, IDataOverlayService dataOverlayService) {
     this.projectBackgroundService = projectBackgroundService;
+    this.dataOverlayService = dataOverlayService;
   }
 
   public List<Map<String, Object>> getModels(String projectId) throws QueryException {
@@ -212,10 +214,7 @@ public class ModelRestImpl extends BaseRestImpl {
       int overlayId = parseInteger(overlayIdString, "overlayId");
       DataOverlay overlay = dataOverlayService.getDataOverlayById(projectId, overlayId);
 
-      ColorSchemaReader reader = new ColorSchemaReader();
-      Collection<DataOverlayEntry> schemas = reader.readColorSchema(overlay.getInputData().getFileContent(),
-          overlay.getColorSchemaType());
-
+      Set<DataOverlayEntry> schemas = overlay.getEntries();
       new ColorModelCommand(part, schemas, getUserService().getColorExtractorForUser(user)).execute();
     }
 

web/src/test/java/lcsb/mapviewer/web/MapControllerIntegrationTest.java

@@ -41,9 +41,9 @@ import lcsb.mapviewer.converter.graphics.PngImageGenerator;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
 import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.layout.ProjectBackground;
 import lcsb.mapviewer.model.map.model.ModelData;
 import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.overlay.DataOverlay;
 import lcsb.mapviewer.model.security.PrivilegeType;
 import lcsb.mapviewer.model.user.User;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
@@ -651,6 +651,28 @@ public class MapControllerIntegrationTest extends ControllerIntegrationTest {
         .andExpect(status().is2xxSuccessful());
   }
 
+  @Test
+  public void testDownloadImageDataOverlay() throws Exception {
+    MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+    DataOverlay overlay = createOverlayInSeparateThread(TEST_PROJECT,
+        userService.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN));
+
+    RequestBuilder request = get("/projects/{projectId}/models/{mapId}:downloadImage?" +
+        "handlerClass={handlerClass}&overlayIds={ids}",
+        TEST_PROJECT,
+        map.getId(),
+        PngImageGenerator.class.getCanonicalName(),
+        overlay.getId())
+            .session(session);
+
+    mockMvc.perform(request)
+        .andDo(document("projects/project_maps/download_image_data_overlay",
+            downloadImageRequestParameters(),
+            mapPathParameters()))
+        .andExpect(status().is2xxSuccessful());
+  }
+
   @Test
   public void testDownloadInfluenceMap() throws Exception {
     MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);